Crystal structure of crystal form 2 of an active KRAS G12D (gppcp) dimer in complex with bi-5747

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 27% strand (DSSP).

Ligands and binding sites

• GCP · Phosphomethylphosphonic acid guanylate ester · ligand · 4 copies · chains A, B, C, D
• R6W · (3~{S})-5-oxidanyl-3-[2-[[6-[[3-[(1~{S})-6-oxidanyl-3-oxidanylidene-1,2-dihydroisoindol-1-yl]-1~{H}-indol-2-yl]methylamino]hexylamino]methyl]-1~{H}-indol-3-yl]-2, 3-dihydroisoindol-1-one · ligand · 2 copies · chains A, D, B, C
• MG · Magnesium ion · metal · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 537 Ų buried · 1 hydrogen bond · protein-protein
• B–C · 270 Ų buried · 4 hydrogen bonds · protein-protein
• A–D · 259 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 7ACF · Crystal structure of crystal form 2 of an active KRAS G12D (gppcp) dimer in complex with… · the same entry in another collection · chain C against C, TM-score 1.00

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P01116
• Elsewhere: RCSB PDB 7ACF · PDBe 7ACF · UniProt P01116